Matteo Barberis

Dr Matteo Barberis


Reader in Systems Biology
PhD (Industrial Biotechnology and Biochemistry), FRSB (Fellow, Royal Society of Biology Council), BSc (Bioinformatics), MSc (Industrial Biotechnology)
+44 (0)1483 684610
07 AX 01
Student feedback and consultation hours: Monday to Friday, 9:30am - 7:30pm (by appointment)

Biography

Areas of specialism

Systems Biology; Cell Cycle Control; Biochemistry; Molecular Biology; Computational Biology; Multi-scale Modeling

Research

Research interests

My publications

Publications

Barberis Matteo, Helikar T., Verbruggen P. (2018)Simulation of stimulation: Cytokine dosage and cell cycle crosstalk driving timing-dependent T cell differentiation, In: Frontiers in Physiology9pp. 879-896 Frontiers Media S.A.
Zhang Y., Kouril T., Snoep J.L., Siebers B., Barberis Matteo, Westerhoff H.V. (2017)The peculiar glycolytic pathway in hyperthermophylic archaea: Understanding its whims by experimentation in silico, In: International Journal of Molecular Sciences18(4) MDPI
Puniya B.L., Todd R.G., Mohammed A., Brown D.M., Barberis Matteo, Helikar T. (2018)A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage, In: Frontiers in Physiology9878pp. 1-18 Frontiers Media S.A.
Abudukelimu A., Mondeel T.D.G.A., Barberis Matteo, Westerhoff H.V. (2017)Learning to read and write in evolution: From static pseudoenzymes and pseudosignalers to dynamic gear shifters, In: Biochemical Society Transactions45(3)pp. 635-652 Portland Press Ltd
Abudukelimu A., Barberis Matteo, Redegeld F.A., Sahin N., Westerhoff H.V. (2018)Predictable irreversible switching between acute and chronic inflammation, In: Frontiers in Immunology91596pp. 1-16 Frontiers Media S.A.
Linke C., Chasapi A., González-Novo A., Al Sawad I., Tognetti S., Klipp E., Loog M., Krobitsch S., Posas F., Xenarios I., Barberis Matteo (2017)A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle, In: npj Systems Biology and Applications3(1) Nature Publishing Group
Mondeel Thierry D G A, Crémazy Frédéric, Barberis Matteo GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae, In: Bioinformatics34(12)pp. 2147-2149 Oxford University Press
Spiesser T.W., Klipp E., Barberis Matteo (2009)A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae, In: Molecular Genetics and Genomics282(1)pp. 25-35 Springer
Barberis Matteo, Spiesser T.W., Klipp E. (2010)Replication origins and timing of temporal replication in budding yeast: How to solve the conundrum?, In: Current Genomics11(3)pp. 199-211 Bentham Science Publishers
Barberis Matteo, Klipp E., Vanoni M., Alberghina L. (2007)Cell size at S phase initiation: An emergent property of the G1/S network, In: PLoS Computational Biology3(4)pp. 649-666 Public Library of Science
Spiesser T.W., Diener C., Barberis Matteo, Klipp E. (2010)What influences DNA replication rate in budding yeast?, In: PLoS ONE5(4)e10203pp. 1-9 Public Library of Science
Barberis Matteo, Pagano M.A., De Gioia L., Marin O., Vanoni M., Pinna L.A., Alberghina L. (2005)CK2 regulates in vitro the activity of the yeast cyclin-dependent kinase inhibitor Sic1, In: Biochemical and Biophysical Research Communications336(4)pp. 1040-1048 Elsevier
Barberis Matteo, Klipp E. (2007)Insights into the network controlling the G1/S transition in budding yeast., In: Genome Informatics 200718(18)pp. 85-99 Japanese Society for Bioinformatics
Alfieri R., Barberis Matteo, Chiaradonna F., Gaglio D., Milanesi L., Vanoni M., Klipp E., Alberghina L. (2009)Towards a systems biology approach to mammalian cell cycle: Modeling the entrance into S phase of quiescent fibroblasts after serum stimulation, In: BMC Bioinformatics10(sup.12) BioMed Central Ltd.
Barberis Matteo, De Gioia L., Ruzzene M., Sarno S., Coccetti P., Fantucci P., Vanoni M., Alberghina L. (2005)The yeast cyclin-dependent kinase inhibitor Sic1 and mammalian p27Kip1 are functional homologues with a structurally conserved inhibitory domain, In: Biochemical Journal387(3)pp. 639-647 Portland Press Ltd
Barberis Matteo, Beck C., Amoussouvi A., Schreiber G., Diener C., Herrmann A., Klipp E. (2011)A low number of SIC1 mRNA molecules ensures a low noise level in cell cycle progression of budding yeast, In: Molecular BioSystems7(10)pp. 2804-2812 Royal Society of Chemistry
Barberis Matteo, Spiesser T.W., Klipp E. (2010)Kinetic modelling of DNA replication initiation in budding yeast., In: Genome Informatics 2010 (Proceedings of the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010), Kyoto University, Japan, 26 – 28 July 2010)(Vol.24)pp. 1-20 Imperial College Press
Mondeel Thierry D.G.A, Ivanov Oleksandr, Westerhoff Hans V., Liebermeister Wolfram, Barberis Matteo Clb3-centered regulations are recurrent across distinctparameter regions in minimal autonomous cell cycle oscillatordesigns, In: NPJ Systems Biology and Applications6(1)8 Nature Research
Abudukelimu Abulikemu, Barberis Matteo, Redegeld Frank, Sahin Nilgun, Sharma Raju P., Westerhoff Hans V. Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity, In: Frontiers in Immunology103091 Frontiers Media
Mondeel Thierry D G A, Holland Petter, Nielsen Jens, Barberis Matteo (2019)ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast, In: Nucleic Acids Research47(15)pp. 7825-7841 Oxford University Press
Barberis Matteo, Chen Lin, Aparicio Oscar M., Ostrow A. Zachary, Linke Christian, Kalhor Reza, Gan Yan, Villwock Sandra K. (2017)Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes inS. cerevisiae, In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA114(12)pp. E2411-E2419 NATL ACAD SCIENCES
Schreiber G., Barberis Matteo, Scolari S., Klaus C., Herrmann A., Klipp E. (2012)Unraveling interactions of cell cycle-regulating proteins Sic1 and B-type cyclins in living yeast cells: A FLIM-FRET approach, In: FASEB Journal26(2)pp. 546-554 Federation of American Society of Experimental Biology (FASEB)
Westerhoff H.V., He F., Murabito E., Crémazy F., Barberis Matteo (2014)Understanding Principles of the Dynamic Biochemical Networks of Life Through Systems Biology, In: Computational Systems Biology: From Molecular Mechanisms to Disease: Second Editionpp. 21-44 Academic Press
Westerhoff H.V., Nakayama S., Mondeel T.D.G.A., Barberis Matteo (2015)Systems Pharmacology: An opinion on how to turn the impossible into grand challenges, In: Drug Discovery Today: Technologies15pp. 23-31 Elsevier
Supady A., Klipp E., Barberis Matteo (2013)A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae, In: Journal of Biotechnology168(2)pp. 174-184 Elsevier
Linke C., Klipp E., Lehrach H., Barberis Matteo, Krobitsch S. Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions, In: Frontiers in Physiology4173 Frontiers Media
Zañudo J.G.T., Naldi A., Thieffry D., Monteiro P.T., Müssel C., Kestler H.A., Xenarios I., Saez-Rodriguez J., Helikar T., Chaouiya C., Albert R., Barberis M., Crespo I., Calzone L., Chasapi A., Cokelaer T., Dorier J., Dräger A., Hernandez C., Hucka M., De Jong H., Keating S.M., Le Novère N., Klamt S., Klarner H., Laubenbacher R., Niknejad A., Rodriguez N., Siebert H., Stoll G. (2015)Cooperative development of logical modelling standards and tools with CoLoMoTo, In: Bioinformatics31(7)pp. 1154-1159 Oxford University Press
Barberis Matteo (2012)Molecular systems biology of sic1 in yeast cell cycle regulation through multiscale modeling, In: Advances in Systems Biology736(736)pp. 135-167 Springer
Barberis Matteo, Todd R.G., van der Zee L. (2017)Advances and challenges in logical modeling of cell cycle regulation: Perspective for multi-scale, integrative yeast cell models, In: FEMS Yeast Research17(1)fow103 Oxford University Press
Barberis Matteo, Linke C., Adrover M.T., González-Novo A., Lehrach H., Krobitsch S., Posas F., Klipp E. Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins, In: Biotechnology Advances30(1)pp. 108-130 Elsevier
Mondeel T.D.G.A., Rehman S., Zhang Y., Verma M., Dürre P., Barberis Matteo, Westerhoff H.V. (2016)Maps for when the living gets tough: Maneuvering through a hostile energy landscape, In: IFAC-PapersOnLine49(26)pp. 364-370 Elsevier
Marangoni F., Barberis Matteo, Botta M. (2003)Large scale prediction of protein interactions by a SVM-based method, In: Proceedings of Neural Nets: 14th Italian Workshop on Neural Nets, WIRN VIETRI 2003, Vietri sul Mare, Italy, June 4-7, 2003, Revised Papers (Lecture Notes in Computer Science)2859pp. 296-301 Springer Verlag